... This is from an RNA Seq experiment right, and you're attempting to call variants? AFAIK, `SplitNCigarReads` corrects the CIGAR string when reads span splice junctions, and forces filters for `MalformedReadFilter` and `ReassignOneMappingQualityFilter`, of which all of your reads seems to have passed. ...

... It's in the Limma Users Guide (Hint: [look at page 101][1]). Try to be more specific with your questions, generally asking for tutorials and commands to blindly run isn't the best way to learn how or why you're doing something.
[1]: https://www.bioconductor.org/packages/3.7/bioc/vignettes/limma ...

... When using basemount, it works no problem for me to retrieve fastq. AFAIK, basemount isn't (or shouldn't be symlinking), the files should appear normally, but are only fully retrieved from base space when a command is carried out on them. I wonder if invoking the `-L` flag in find is treating them a ...

... You can run Joint genotyping on as little as 2 samples (ASAIK - If anyone has a link to contradict me, please share!), however it's the variant filtering stage that you may have trouble with. [In the GATK forums it's recommended that to use VQSR, at least 30 whole exome samples or 1 whole genome sam ...

... You don't have to re-do the processing from MuTect2, but use GATK's [SelectVariants][1] to filter through your call set.
[1]: https://software.broadinstitute.org/gatk/gatkdocs/3.7-0/org_broadinstitute_gatk_tools_walkers_variantutils_SelectVariants.php ...